http://2012.igem.org/wiki/index.php?title=Special:Contributions/Rahmilale&feed=atom&limit=50&target=Rahmilale&year=&month=2012.igem.org - User contributions [en]2024-03-28T17:23:23ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:NTNU_Trondheim/Templates/Calendar/MayTeam:NTNU Trondheim/Templates/Calendar/May2013-06-20T10:38:20Z<p>Rahmilale: </p>
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<div><!--<br />
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{| align="center" style="text-align:right;" cellpadding="3"<br />
|+ <b> [https://2012.igem.org/Team:NTNU_Trondheim/Notebook/May May] </b><br />
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|[https://2012.igem.org/Team:NTNU_Trondheim/Notebook/May#Wednesday_02.05.12 2]<br />
|[https://2012.igem.org/Team:NTNU_Trondheim/Notebook/May#Thursday_03.05.12 3]<br />
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|[https://2012.igem.org/Team:NTNU_Trondheim/Notebook/May#Wednesday_09.05.12 9]<br />
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|[https://2012.igem.org/Team:NTNU_Trondheim/Notebook/May#Friday_18.05.12 18]<br />
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|21<br />
|22<br />
|[https://2012.igem.org/Team:NTNU_Trondheim/Notebook/May#Wednesday_23.05.12 23]<br />
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|[https://2012.igem.org/Team:NTNU_Trondheim/Notebook/May#Friday_25.05.12 25]<br />
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|}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/TeamTeam:NTNU Trondheim/Team2012-09-26T21:30:05Z<p>Rahmilale: </p>
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<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
__NOTOC__<br />
<html><br />
<div class="container"><br />
<div class="page-header-top"><br />
<h1>Meet the team <small> Team NTNU Trondheim up close and personal</small></h1><br />
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<div class="container main-container"><br />
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<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/ove_nina.png" alt=""><br />
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</div><br />
</div><br />
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<div class="page-header"><br />
<h1>The students</h1><br />
</div><br />
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<div class="row-fluid"><br />
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<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/gunvor.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>Graduated M.Sc. in Chemical engineering and biotechnology from NTNU, with specialization in biotechnology. <!--So now, I'm a graduate engineer (yay!). In my master thesis, I investigated the interaction between DNA and Uracil DNA Glycosylase, which is a repair enzyme removing uracil from DNA, using optical tweezers. I also just recieved a research stipend in medical imaging, meaning that for the next semester, I'll continue investigating single molecule interactions using optical tweezers.--></dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Gunvor Røkke</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Mainly playing the violin. I have been playing since I was five years old, and I am currently leading one of the three folk music orchestras in Trondheim. I also like to swim, or to gab with my friends.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>Team leader:</i> Teaching the other team members the basic cloning techniques used for biobrick assembly.</li><br />
<li><i>Team representative:</i> In case of interested journalists, I will talk to them. Rolf will be my manager and Nina my stylist! </li><br />
<li><i>Team dietitian:</i> One of my less serious responsibility areas is to make sure that all team members get their daily dose of carbohydrates (as we all agree that lowcarb is nonsense).</li></dd><br />
<dt>Fun fact:</dt><dd>I'm able to whistle and hum in two part harmony with myself. And no, I'm not mutated.</dd><br />
</dl><br />
</div><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/nina.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Eidsvåg, Møre og Romsdal</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Nina Hole</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Sports enthusiast, but especially interested in football. I also play football myself on NTNU's own football team. Other interests are reading, traveling and food.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul><li><i>Gunvor's stylist</i>:If Gunvor is representing the team, I have the main responsibility to do her make-up and so on.</li><li><i>Photo chief</i>: If something needs photographing, Nina is on the job!</li></ul><br />
</dd><br />
<dt>Fun fact:</dt><dd><br />
My favorite author/musician Jo Nesbø, has named his main character in his criminal novels Harry Hole. His inspiration for the last name comes from my family! </dd><br />
</dl><br />
</div><br />
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<div class="row-fluid"><br />
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<div class="span2"><br />
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<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/jarle.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Drammen</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Jarle Pahr</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Aikido and psychology.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul><li><i>Master of the notebook:</i> Trying to get the other team members to update the notebook.</li><li><i>Cake chief: </i> Baking awesome cakes.</li></ul></dd><br />
<dt>Fun fact:</dt><dd>Is resistant to norovirus, thanks to a mutation in the FUT2 gene. Being a mutant is nice!</dd><br />
</dl><br />
</div><br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/eirin.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Larvik</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Eirin Korvald</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Music (both playing and listening), snowboarding, hiking, knitting, hanging with friends.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>iGEM hair dresser:</i> Making sure the entire team has fabulous hair at all times.</li></dd><br />
</dl><br />
</div><br />
</div><br />
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<br />
<div class="row-fluid"><br />
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<div class="span2"><br />
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<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/ove.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Ove Øyås</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Nature, cycling, hiking, music, programming, being enthusiastic about stuff.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>Internet chief:</i> Fixing the wiki and the Matchmaker. Making spaghetti code.</li></dd><br />
<dt>Fun fact:</dt><dd>Will easily eat raw ginger and garlic.</dd><br />
</dl><br />
</div><br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/rolf.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in applied theoretical chemistry.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Rolf Heilemann Myhre</h2><br />
<dl><br />
<dt>Interests outside Academia:</dt><dd>In my spare time, I like exercising, hanging with friends, partying, movies etc. Also, I can't live without my computer.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul>Modelling the genetic circuit.</dd><br />
<dt>Fun fact:</dt><dd>I have not studied any biotechnology before joining the iGEM team.</dd><br />
</dl><br />
</div><br />
</div><br />
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<br />
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<div class="page-header"><br />
<h1>The advisors</h1><br />
</div><br />
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<div class="row-fluid"><br />
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<div class="span2"><br />
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<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/eivind.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Stavanger, Norway</dd><br />
<dt>Position:</dt><dd>Professor</dd><br />
</div> <br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Eivind Almaas</h2><br />
<dl><br />
<dt>Area of expertise:</dt><dd>Systems biology and network analysis</dd><br />
<dt>Interests outside academia:</dt><dd>Hiking, reading, living.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li>Team organization.</li><li>Computer modelling.</li></dd><br />
<dt>Fun fact:</dt><dd>Big fan of 50's Rock'n Roll and Rockabilly.</dd><br />
<br />
<br />
<br />
</dl><br />
</div><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/rahmi.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Cologne, Germany</dd><br />
<dt>Position:</dt><dd>Postdoctoral fellow</dd><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Rahmi Lale</h2><br />
<dl><br />
<dt>Area of expertise:</dt><dd>Transcriptional and translational regulation of bacterial gene<br />
expression, metabolic engineering. Metagenome/biodiscovery.</dd><br />
<dt>Interests outside academia:</dt><dd> Loves playing bass, likes biking/hiking/skiing/fishing/sailing, into web/graphic design.</dd><br />
<dt>Areas of responsibility:</dt><dd>Herding the nerds!</dd><br />
<dt>Fun fact:</dt><dd>He loves bugs so much that he makes his own kefir.</dd><br />
</dl><br />
</div><br />
<br />
</div><br />
<br />
<div class="row-fluid"><br />
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<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/martin.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Mannheim, Germany</dd><br />
<dt>Position:</dt><dd>Associate professor</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Martin Hohmann-Marriott</h2><br />
<dl><br />
<dt>Area of expertise:</dt><dd>Photosynthesis, bioenergetics, molecular biology.</dd><br />
<dt>Interests outside academia:</dt><dd>My family, history, all things computer and technology</dd><br />
<dt>Areas of responsibility:</dt><dd>Instructor, molecular biology and physiology<br />
</dd><br />
<dt>Fun fact:</dt><dd>Martin designed exercise equipment for ants as an undergraduate.</dd><br />
</dl><br />
</div><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/marius.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Kristiansand, Norway</dd><br />
<dt>Position:</dt><dd>Doctoral student. Graduated M.Sc. in Physics and mathematics from NTNU.</dd><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Marius Eidsaa</h2><br />
<dl><br />
<br />
<dt>Area of expertise:</dt><dd>Systems biology, mainly focusing on networks, both generally and in biology. I'm currently working on network methods and analysis of microarray data..</dd><br />
<dt>Interests outside academia:</dt><dd>I like to sing, and I'm currently singing tenor in two student-society based choirs. Other interests include music in general, food and drink and good company.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li>I'm a modelling instructor, so my main responsibility is to help set up and analyze our model.</li></dd><br />
<dt>Fun fact:</dt><dd>Has been swimming at a national level.</dd><br />
</dl><br />
</div><br />
<br />
</div><br />
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{{:Team:NTNU_Trondheim/Templates/Sponsors}}<br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/TeamTeam:NTNU Trondheim/Team2012-09-26T21:28:51Z<p>Rahmilale: </p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
__NOTOC__<br />
<html><br />
<div class="container"><br />
<div class="page-header-top"><br />
<h1>Meet the team <small> Team NTNU Trondheim up close and personal</small></h1><br />
</div><br />
</div><br />
<br />
<div class="container main-container"><br />
<br />
<br />
<div class="row-fluid"><br />
<br />
<div class="span10 offset1"><br />
<br />
<br />
<div id="myCarousel2" class="carousel slide"><br />
<div class="carousel-inner"><br />
<div class="item active"><br />
<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/team1.png" alt=""><br />
</div><br />
<div class="item"><br />
<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/ove_nina.png" alt=""><br />
</div><br />
<div class="item"><br />
<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/rolf_gunvor.png" alt=""><br />
</div><br />
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<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/eirin_jarle.png" alt=""><br />
</div><br />
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<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/team2.png" alt=""><br />
</div><br />
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<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/run1.png" alt=""><br />
</div><br />
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<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/run2.png" alt=""><br />
</div><br />
<div class="item"><br />
<img src="http://folk.ntnu.no/oyas/igem3/img/team/carousel/run3.png" alt=""><br />
</div><br />
</div><br />
<br />
</div><br />
</div><br />
</div><br />
<br />
<div class="page-header"><br />
<h1>The students</h1><br />
</div><br />
<br />
<div class="row-fluid"><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/gunvor.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>Graduated M.Sc. in Chemical engineering and biotechnology from NTNU, with specialization in biotechnology. <!--So now, I'm a graduate engineer (yay!). In my master thesis, I investigated the interaction between DNA and Uracil DNA Glycosylase, which is a repair enzyme removing uracil from DNA, using optical tweezers. I also just recieved a research stipend in medical imaging, meaning that for the next semester, I'll continue investigating single molecule interactions using optical tweezers.--></dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Gunvor Røkke</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Mainly playing the violin. I have been playing since I was five years old, and I am currently leading one of the three folk music orchestras in Trondheim. I also like to swim, or to gab with my friends.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>Team leader:</i> Teaching the other team members the basic cloning techniques used for biobrick assembly.</li><br />
<li><i>Team representative:</i> In case of interested journalists, I will talk to them. Rolf will be my manager and Nina my stylist! </li><br />
<li><i>Team dietitian:</i> One of my less serious responsibility areas is to make sure that all team members get their daily dose of carbohydrates (as we all agree that lowcarb is nonsense).</li></dd><br />
<dt>Fun fact:</dt><dd>I'm able to whistle and hum in two part harmony with myself. And no, I'm not mutated.</dd><br />
</dl><br />
</div><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/nina.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Eidsvåg, Møre og Romsdal</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Nina Hole</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Sports enthusiast, but especially interested in football. I also play football myself on NTNU's own football team. Other interests are reading, traveling and food.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul><li><i>Gunvor's stylist</i>:If Gunvor is representing the team, I have the main responsibility to do her make-up and so on.</li><li><i>Photo chief</i>: If something needs photographing, Nina is on the job!</li></ul><br />
</dd><br />
<dt>Fun fact:</dt><dd><br />
My favorite author/musician Jo Nesbø, has named his main character in his criminal novels Harry Hole. His inspiration for the last name comes from my family! </dd><br />
</dl><br />
</div><br />
<br />
</div><br />
<div class="row-fluid"><br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/jarle.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Drammen</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Jarle Pahr</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Aikido and psychology.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul><li><i>Master of the notebook:</i> Trying to get the other team members to update the notebook.</li><li><i>Cake chief: </i> Baking awesome cakes.</li></ul></dd><br />
<dt>Fun fact:</dt><dd>Is resistant to norovirus, thanks to a mutation in the FUT2 gene. Being a mutant is nice!</dd><br />
</dl><br />
</div><br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/eirin.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Larvik</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Eirin Korvald</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Music (both playing and listening), snowboarding, hiking, knitting, hanging with friends.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>iGEM hair dresser:</i> Making sure the entire team has fabulous hair at all times.</li></dd><br />
</dl><br />
</div><br />
</div><br />
<br />
<br />
<div class="row-fluid"><br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/ove.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Ove Øyås</h2><br />
<dl><br />
<dt>Interests outside academia:</dt><dd>Nature, cycling, hiking, music, programming, being enthusiastic about stuff.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>Internet chief:</i> Fixing the wiki and the Matchmaker. Making spaghetti code.</li></dd><br />
<dt>Fun fact:</dt><dd>Will easily eat raw ginger and garlic.</dd><br />
</dl><br />
</div><br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/rolf.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in applied theoretical chemistry.</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Rolf Heilemann Myhre</h2><br />
<dl><br />
<dt>Interests outside Academia:</dt><dd>In my spare time, I like exercising, hanging with friends, partying, movies etc. Also, I can't live without my computer.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul>Modelling the genetic circuit.</dd><br />
<dt>Fun fact:</dt><dd>I have not studied any biotechnology before joining the iGEM team.</dd><br />
</dl><br />
</div><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<div class="page-header"><br />
<h1>The advisors</h1><br />
</div><br />
<br />
<div class="row-fluid"><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/eivind.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Stavanger, Norway</dd><br />
<dt>Position:</dt><dd>Professor</dd><br />
</div> <br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Eivind Almaas</h2><br />
<dl><br />
<dt>Area of expertise:</dt><dd>Systems biology and network analysis</dd><br />
<dt>Interests outside academia:</dt><dd>Hiking, reading, living.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li>Team organization.</li><li>Computer modelling.</li></dd><br />
<dt>Fun fact:</dt><dd>Big fan of 50's Rock'n Roll and Rockabilly.</dd><br />
<br />
<br />
<br />
</dl><br />
</div><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/rahmi.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Cologne, Germany</dd><br />
<dt>Position:</dt><dd>Postdoc.</dd><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Rahmi Lale</h2><br />
<dl><br />
<dt>Area of expertise:</dt><dd>Transcriptional and translational regulation of bacterial gene<br />
expression, metabolic engineering. Metagenome/biodiscovery.</dd><br />
<dt>Interests outside academia:</dt><dd> Loves playing bass, likes biking/hiking/skiing/fishing/sailing, into web/graphic design.</dd><br />
<dt>Areas of responsibility:</dt><dd>Herding the nerds!</dd><br />
<dt>Fun fact:</dt><dd>He loves bugs so much that he makes his own kefir.</dd><br />
</dl><br />
</div><br />
<br />
</div><br />
<br />
<div class="row-fluid"><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/martin.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Mannheim, Germany</dd><br />
<dt>Position:</dt><dd>Associate professor</dd></div><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Martin Hohmann-Marriott</h2><br />
<dl><br />
<dt>Area of expertise:</dt><dd>Photosynthesis, bioenergetics, molecular biology.</dd><br />
<dt>Interests outside academia:</dt><dd>My family, history, all things computer and technology</dd><br />
<dt>Areas of responsibility:</dt><dd>Instructor, molecular biology and physiology<br />
</dd><br />
<dt>Fun fact:</dt><dd>Martin designed exercise equipment for ants as an undergraduate.</dd><br />
</dl><br />
</div><br />
<br />
<br />
<div class="span2"><br />
<br />
<a href="#"><img alt="" src="http://folk.ntnu.no/oyas/igem3/img/team/marius.png" class="img-circle"></a><br />
<dl><div class="well well-small"><br />
<dt>Origin of replication:</dt><dd>Kristiansand, Norway</dd><br />
<dt>Position:</dt><dd>Doctoral student. Graduated M.Sc. in Physics and mathematics from NTNU.</dd><br />
</dl><br />
</div><br />
<div class="span4"><br />
<h2>Marius Eidsaa</h2><br />
<dl><br />
<br />
<dt>Area of expertise:</dt><dd>Systems biology, mainly focusing on networks, both generally and in biology. I'm currently working on network methods and analysis of microarray data..</dd><br />
<dt>Interests outside academia:</dt><dd>I like to sing, and I'm currently singing tenor in two student-society based choirs. Other interests include music in general, food and drink and good company.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li>I'm a modelling instructor, so my main responsibility is to help set up and analyze our model.</li></dd><br />
<dt>Fun fact:</dt><dd>Has been swimming at a national level.</dd><br />
</dl><br />
</div><br />
<br />
</div><br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/OutreachTeam:NTNU Trondheim/Outreach2012-09-26T21:17:23Z<p>Rahmilale: /* Human practices in summary */</p>
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<div class="container"><br />
<div class="page-header-top"><br />
<h1>Human practices <small>Bringing synthetic biology to the masses</small></h1><br />
</div><br />
</div><br />
<br />
<br />
<div class="container main-container"><br />
</html><br />
__TOC__<br />
==Human practices in summary==<br />
<br />
Our main human practices project will be to participate in Researchers' Night, which is an event for high school students and students from non-degree granting colleges. The goal of researchers' night is to show the students that research is fun, to inspire them, and to motivate them to take higher education.<br />
As a second outreach project, the team will be writing a chapter on different biobrick assembly methods in a textbook. <br />
<br />
We also concider our Matchmaker an important part of our outreach effort. Read more about it [https://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Collaboration&action=submit#The_iGEM_Matchmaker here].<br />
<br />
==Researchers' Night==<br />
<br />
This year, the NTNU iGEM team is participating in Researchers' Night, which is an arrangement for high school students. This is the eighth year Researchers' night is being arranged, and it has traditionally been very popular at NTNU. Last year, over 1200 students visited the arrangement. This year, Researchers' night will be arranged the 28th of september, and we have been inveted to participate. We are really looking forward to it, since this is a unique opportunity to tell students about the possibilities of synthetic biology, and motivate them for a career in biotechnology. It seems that the students are looking forward to it as well, since this year's arrangement was fully booked in 4 minutes! Some photos from last year's event (taken by Kristina Jones, NTNU) can be seen in the carousel below.<br />
<br />
<br />
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<a class="left carousel-control" href="#myCarousel2" data-slide="prev">&lsaquo;</a><br />
<a class="right carousel-control" href="#myCarousel2" data-slide="next">&rsaquo;</a><br />
<br />
</div><br />
</div><br />
</div><br />
</html><br />
<br />
This year, the 1100 participating students can visit 31 different stands, one of them being ours. To get the students to understand the concept of giving organisms new characteristic properties by putting together biobricks, we have made a biobrick construction kit, including both DNA and restriction enzymes (a picture of the DNA from the construction kit is given below). We hope that this construction kit will make it easier both to understand why we are able to put together biobricks using certain combinations of restriction enzymes, and we also hope we can teach them what the different sequences that makes a gene are used for.<br />
<br />
[[File:BiobrikkeByggesett.png|400px|thumb|center|Our BioBrick construction kit]]<br />
<br />
==Text book chapter on biobrick assembly methods==<br />
<br />
Early in the semester, we were asked by our advisor, Rahmi Lale, to write a chapter on biobrick assembly methods for a text book he and Svein Valla, Professor at Dept. of Biotechnology, NTNU, are editing. The text book in question is called 'DNA cloning methods', and is part of the book series '[http://www.springer.com/series/7651 Methods in Molecular Biology]' published by Humana Press. We will finalise the chapter after the Europe Regional Jamboree.<br />
<br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/OutreachTeam:NTNU Trondheim/Outreach2012-09-26T21:16:25Z<p>Rahmilale: /* Text book chapter on biobrick assembly methods */</p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<html><br />
<div class="container"><br />
<div class="page-header-top"><br />
<h1>Human practices <small>Bringing synthetic biology to the masses</small></h1><br />
</div><br />
</div><br />
<br />
<br />
<div class="container main-container"><br />
</html><br />
__TOC__<br />
==Human practices in summary==<br />
<br />
Our main human practices project will be to participate in Researchers' Night, which is an event for high school students and students from non-degree granting colleges. The goal of researchers' night is to show the students that research is fun, to inspire them, and to motivate them to take higher education.<br />
As a second outreach project, the team will be writing a chapter on different biobrick assembly methods in a textbook. <br />
<br />
We also concider our Matchmaker an important part of our outreach effort. Read more about it [https://2012.igem.org/wiki/index.php?title=Team:NTNU_Trondheim/Collaboration&action=submit#The_iGEM_Matchmaker here]<br />
<br />
==Researchers' Night==<br />
<br />
This year, the NTNU iGEM team is participating in Researchers' Night, which is an arrangement for high school students. This is the eighth year Researchers' night is being arranged, and it has traditionally been very popular at NTNU. Last year, over 1200 students visited the arrangement. This year, Researchers' night will be arranged the 28th of september, and we have been inveted to participate. We are really looking forward to it, since this is a unique opportunity to tell students about the possibilities of synthetic biology, and motivate them for a career in biotechnology. It seems that the students are looking forward to it as well, since this year's arrangement was fully booked in 4 minutes! Some photos from last year's event (taken by Kristina Jones, NTNU) can be seen in the carousel below.<br />
<br />
<br />
<html><br />
<div class="row"><br />
<div class="span8 offset2"><br />
<div id="myCarousel2" class="carousel slide"><br />
<div class="carousel-inner"><br />
<div class="item active"><br />
<img src="http://folk.ntnu.no/gunvor/iGEM/RN1.PNG" alt=""><br />
</div><br />
<div class="item"><br />
<img src="http://folk.ntnu.no/gunvor/iGEM/RN2.PNG" alt=""><br />
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<img src="http://folk.ntnu.no/gunvor/iGEM/RN3.PNG" alt=""><br />
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<img src="http://folk.ntnu.no/gunvor/iGEM/RN4.PNG" alt=""><br />
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<img src="http://folk.ntnu.no/gunvor/iGEM/RN5.PNG" alt=""><br />
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<img src="http://folk.ntnu.no/gunvor/iGEM/RN6.PNG" alt=""><br />
</div><br />
<div class="item"><br />
<img src="http://folk.ntnu.no/gunvor/iGEM/RN7.PNG" alt=""><br />
</div><br />
</div><br />
<a class="left carousel-control" href="#myCarousel2" data-slide="prev">&lsaquo;</a><br />
<a class="right carousel-control" href="#myCarousel2" data-slide="next">&rsaquo;</a><br />
<br />
</div><br />
</div><br />
</div><br />
</html><br />
<br />
This year, the 1100 participating students can visit 31 different stands, one of them being ours. To get the students to understand the concept of giving organisms new characteristic properties by putting together biobricks, we have made a biobrick construction kit, including both DNA and restriction enzymes (a picture of the DNA from the construction kit is given below). We hope that this construction kit will make it easier both to understand why we are able to put together biobricks using certain combinations of restriction enzymes, and we also hope we can teach them what the different sequences that makes a gene are used for.<br />
<br />
[[File:BiobrikkeByggesett.png|400px|thumb|center|Our BioBrick construction kit]]<br />
<br />
==Text book chapter on biobrick assembly methods==<br />
<br />
Early in the semester, we were asked by our advisor, Rahmi Lale, to write a chapter on biobrick assembly methods for a text book he and Svein Valla, Professor at Dept. of Biotechnology, NTNU, are editing. The text book in question is called 'DNA cloning methods', and is part of the book series '[http://www.springer.com/series/7651 Methods in Molecular Biology]' published by Humana Press. We will finalise the chapter after the Europe Regional Jamboree.<br />
<br />
<br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/PressTeam:NTNU Trondheim/Press2012-09-26T20:51:19Z<p>Rahmilale: /* gemFM */</p>
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<div class="container"><br />
<div class="page-header-top"><br />
<h1>Press coverage <small>NTNU iGEM in the media</small></h1><br />
</div><br />
</div><br />
<br />
<br />
<div class="container main-container"><br />
</html><br />
<br />
Our team has being featured in several different media this year. <br />
All the published articles about us, in addition interviews with team members are listed below. <br />
<br />
===NTNU's main website===<br />
<br />
NTNU has written an [http://www.ntnu.no/aktuelt/igemntnu2012 article] about the team and the project on their main website.<br />
<br />
===Under Dusken===<br />
<br />
The student newspaper in Trondheim, Under Dusken, visited us in the lab and wrote an article about us, the project, and iGEM in general.<br />
<br />
[[File:Under_Dusken.jpg|thumb|center|350px]]<br />
<br />
===Bioteknologinemda===<br />
<br />
Bioteknologinemda (in english; the biotechnology committee), which is a committee appointed by the Norwegian government to assist in matters dealing with biotechnology, have published an [http://www.bion.no/2012/09/vil-sende-bakterier-mot-kreftcellene/ interview] with our team leader, Gunvor, on their website. The interview will also be published in their periodical, GEN<i>i</i>alt.<br />
<br />
===VG===<br />
<br />
This year, our team will be participating in Researchers' Night as our main outreach project (read more about this on our [https://2012.igem.org/Team:NTNU_Trondheim/Outreach outreach] page), and in this context, we have also been featured in an article. The Norwegian Science Week, which Researchers' Night is a part of, have cooperated with Verdens Gang (abbreviated VG, Norway's biggest newspaper) to make a magazine covering some of the most interesting activities (we think) that is going to be part of the Science Week. This magazine will be given out as an appendix to the newspaper, and we are one of very few research activities taking part in Science Week Trondheim that have been featured. The article can be read below.<br />
<br />
[[File:Forskningsdagene_VG.PNG|thumb|center|350px]]<br />
<br />
===gemFM===<br />
<br />
We were interviewed by the University College London iGEM team's radio channel, gemFM. Click [https://2012.igem.org/Team:University_College_London/gemFM here] to listen to their shows.<br />
<br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/Experiments_and_ResultsTeam:NTNU Trondheim/Experiments and Results2012-09-26T20:47:20Z<p>Rahmilale: /* Regulative LacI generator (BBa_K822004) */</p>
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<h1>Experiments and results <small>How we tested our components and what we found out</small></h1><br />
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__TOC__<br />
<br />
==Experiments and results==<br />
<br />
To make a genetic circuit releasing colicin as a response to a low oxygen level and a high lactate level, we needed several biobricks. For a detailed list of all biobricks present in our construct, see the [https://2012.igem.org/Team:NTNU_Trondheim/Biobricks biobricks page]. A sketch showing our final construct built from all the necessary biobricks is also given below:<br />
<br />
* Bilde<br />
<br />
Most of the biobricks we decided to use were already present in the registry, but we also needed biobricks with certain properties that were not present in the registry. These we had to make ourselves. The new bricks we made, and which we also characterized, are the following; <br />
<br />
. a protein coding brick for colicin E1, <br />
<br />
. a YFP-generator, a regulative LacI-generator, which is also an improvement of an already existing biobrick, <br />
<br />
. the lld promotor + RBS from ''E.coli'', <br />
<br />
. and the lld promotor + RBS from ''C.glutamicum''.<br />
<br />
This page will focus on the biobricks we have made, how we made them, and how we have characterized them to show that they work.<br />
<br />
<br />
===Colicin (<partinfo>BBa_K822002</partinfo>)===<br />
<br />
Colicin is the protein we have chosen as toxin in our bacterial anti-cancer-kamikaze device. <br />
<br />
<br />
===Regulative LacI generator (<partinfo>BBa_K822004</partinfo>)===<br />
<br />
We made this brick in an effort to improve an already existing biobrick. The brick we wanted to improve was <partinfo>BBa_K292006</partinfo>. The NTNU iGEM team 2011 tried to use this brick in their stress sensor, but did not get it to work. They also tried to test-cut it and investigate the fragments using gel electrophoresis, however the resulting fragments were not as expected. This is why we thought of this biobrick as a suitable candidate for improvement. <br />
Since it is a composite part, we cloned it together again from scratch, using RBS (<partinfo>BBa_B0030</partinfo>), LacI (<partinfo>BBa_C0012</partinfo>) and a double terminator (<partinfo>BBa_B0014</partinfo>).<br />
<br />
When the cloning work was done, we sent both our new biobrick and the old one (<partinfo>BBa_K292006</partinfo>) to sequencing. The sequencing results can be found [https://2012.igem.org/Team:NTNU_Trondheim/Sequencing_Improved_Construct here]. The sequencing result shows that in the old biobrick, only the terminator is present, and no LacI or RBS. In our improved biobrick, both RBS, LacI and terminator are present.<br />
<br />
Both <partinfo>BBa_K822004</partinfo> and <partinfo>BBa_K292006</partinfo> was also investigated using gel electrophoresis. The gel pictures are given below:<br />
<br />
{|border="0"<br />
|[[File:Testkutt_BBa_K292006.png|x300px]]<br />
|[[File:RBS+LacI+term-gel.PNG|x300px]]<br />
|-<br />
|This is the test cut of BBa_K292006 that the NTNU iGEM team 2011 performed. The testcut was performed with EcoRI+PstI (expected fragments: 1303 bp + 2053 bp), BglI+BclI (expected fragments: 1324 bp + 2032 bp), BglI+EcoRV (expected fragments: 1596 bp + 1760 bp) and BglI+BanII (expected fragments: 1521 bp + 1835 bp). The test cut shows that none of the expected fragments are present.<br />
|Test cut of our improved part performed with NotI (first red box, expected fragments: 1276 bp + 2055 bp) and XbaI+PstI (second red box, expected fragments: 1278 bp + 2053 bp). The fragments cut with NotI makes sense on gel. In the case of cutting with XbaI+PstI, we did not expect three fragments, but the upper fragment could be uncut plasmid, since the lower fragments makes sense. <br />
|}<br />
<br />
===lld promoter + RBS from ''E.coli'' (<partinfo>BBa_K822000</partinfo>)===<br />
<br />
The two criteria we wanted fulfilled to initiate lysis and subsequent release of colicin were a low oxygen level and a high lactate level. A promoter activated by low oxygen level was already present in the registry (microaerobic Vgb promoter, <partinfo>BBa_K561001</partinfo>), but we found no suitable lactate-induced promoter. Therefore, we decided to convert the promotor regulating the lldPRD operon in ''E.coli'' into a biobrick, and to use this biobrick in our project [[http://www.ncbi.nlm.nih.gov/pubmed/18263722 1]].<br />
<br />
The primers used to amplify the sequence are given below:<br />
<br />
{|border="1"<br />
!Primer<br />
!Sequence<br />
|-<br />
|Plld EcR fwd<br />
|GTTTCTTCGAATTCGCGGCCGCTTCTAGAGcacattcctataggccgagtaaggt<br />
|-<br />
|Plld EcR rev<br />
|GTTTCTTCCTGCAGCGGCCGCTACTAGTAtgcaggtctcctggagtccacgc<br />
|}<br />
<br />
The capitalized letters of the primer sequences corresponds to the biobrick prefix and suffix. As template, we used the ''E.coli K12'' genome sequence provided by the NCBI nucleotide database [[http://www.ncbi.nlm.nih.gov/nuccore/U00096.2 2]]. These primers in combination with the genome from ''E.coli'' K12 MG1655, yielded a biobrick consisting of the lld promoter including RBS (We called this brick Plld EcR, Ec because it is amplified from ''E.coli'', R because it contains RBS).<br />
<br />
We did not have sufficient time to test the Plld EcR biobrick, but it was sent to sequencing in the official shipping plasmid, pSB1C3, and the sequencing result had a 100 % match with the theoretical sequence of the amplified Plld + RBS sequence in pSB1C3.<br />
<br />
<br />
===ldhA promoter + RBS from ''C.glutamicum'' (<partinfo>BBa_K822001</partinfo>)===<br />
<br />
We also amplified the ldhA promoter from ''Corynebacterium glutamicum''. This has similar properties as the lld promoter from ''E.coli'', so this promoter was also a candidate to being used as the lactate inducable promoter in our project.<br />
The ldhA promoter was amplified using the genome of ''C.glutamicum'' ATC 13032 as template, and the primers below:<br />
<br />
{|border="1"<br />
!Primer<br />
!Sequence<br />
|-<br />
|Plld CgR fwd<br />
|GTTTCTTCGAATTCGCGGCCGCTTCTAGAGctctgttgcttaaat<br />
|-<br />
|Plld CgR rev<br />
|GTTTCTTCCTGCAGCGGCCGCTACTAGTAggtgacctcttctctgaaacgg<br />
|}<br />
<br />
The promoter has not been properly characterized, but sequencing indicated a 100 % match with the theoretical sequence.<br />
<br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/Experiments_and_ResultsTeam:NTNU Trondheim/Experiments and Results2012-09-26T20:45:01Z<p>Rahmilale: /* Experiments and results */</p>
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<div class="container"><br />
<div class="page-header-top"><br />
<h1>Experiments and results <small>How we tested our components and what we found out</small></h1><br />
</div><br />
</div><br />
<br />
<br />
<div class="container main-container"><br />
</html><br />
__TOC__<br />
<br />
==Experiments and results==<br />
<br />
To make a genetic circuit releasing colicin as a response to a low oxygen level and a high lactate level, we needed several biobricks. For a detailed list of all biobricks present in our construct, see the [https://2012.igem.org/Team:NTNU_Trondheim/Biobricks biobricks page]. A sketch showing our final construct built from all the necessary biobricks is also given below:<br />
<br />
* Bilde<br />
<br />
Most of the biobricks we decided to use were already present in the registry, but we also needed biobricks with certain properties that were not present in the registry. These we had to make ourselves. The new bricks we made, and which we also characterized, are the following; <br />
<br />
. a protein coding brick for colicin E1, <br />
<br />
. a YFP-generator, a regulative LacI-generator, which is also an improvement of an already existing biobrick, <br />
<br />
. the lld promotor + RBS from ''E.coli'', <br />
<br />
. and the lld promotor + RBS from ''C.glutamicum''.<br />
<br />
This page will focus on the biobricks we have made, how we made them, and how we have characterized them to show that they work.<br />
<br />
<br />
===Colicin (<partinfo>BBa_K822002</partinfo>)===<br />
<br />
Colicin is the protein we have chosen as toxin in our bacterial anti-cancer-kamikaze device. <br />
<br />
<br />
===Regulative LacI generator (<partinfo>BBa_K822004</partinfo>)===<br />
<br />
We made this brick in an effort to improve an already existing biobrick. The brick we wanted to improve was <partinfo>BBa_K292006</partinfo>. The NTNU iGEM team 2011 tried to use this brick in their stress sensor, but did not get it to work. They also tried to test-cut it and investigate the fragments using gel electrophoresis, but the fragments were either not as expected. This is why we thought this biobrick was a good candidate for an improvement. <br />
Since it is a composite part, we cloned it together again from scratch, using RBS (<partinfo>BBa_B0030</partinfo>), LacI (<partinfo>BBa_C0012</partinfo>) and a double terminator (<partinfo>BBa_B0014</partinfo>).<br />
<br />
When the cloning work was done, we sent both our new biobrick and the old one (<partinfo>BBa_K292006</partinfo>) to sequencing. The sequencing results can be found [https://2012.igem.org/Team:NTNU_Trondheim/Sequencing_Improved_Construct here]. The sequencing result shows that in the old biobrick, only the terminator is present, and no LacI or RBS. In our improved biobrick, both RBS, LacI and terminator are present.<br />
<br />
Both <partinfo>BBa_K822004</partinfo> and <partinfo>BBa_K292006</partinfo> was also investigated using gel electrophoresis. The gel pictures are given below:<br />
<br />
{|border="0"<br />
|[[File:Testkutt_BBa_K292006.png|x300px]]<br />
|[[File:RBS+LacI+term-gel.PNG|x300px]]<br />
|-<br />
|This is the test cut of BBa_K292006 that the NTNU iGEM team 2011 performed. The testcut was performed with EcoRI+PstI (expected fragments: 1303 bp + 2053 bp), BglI+BclI (expected fragments: 1324 bp + 2032 bp), BglI+EcoRV (expected fragments: 1596 bp + 1760 bp) and BglI+BanII (expected fragments: 1521 bp + 1835 bp). The test cut shows that none of the expected fragments are present.<br />
|Test cut of our improved part performed with NotI (first red box, expected fragments: 1276 bp + 2055 bp) and XbaI+PstI (second red box, expected fragments: 1278 bp + 2053 bp). The fragments cut with NotI makes sense on gel. In the case of cutting with XbaI+PstI, we did not expect three fragments, but the upper fragment could be uncut plasmid, since the lower fragments makes sense. <br />
|}<br />
<br />
<br />
===lld promoter + RBS from ''E.coli'' (<partinfo>BBa_K822000</partinfo>)===<br />
<br />
The two criteria we wanted fulfilled to initiate lysis and subsequent release of colicin were a low oxygen level and a high lactate level. A promoter activated by low oxygen level was already present in the registry (microaerobic Vgb promoter, <partinfo>BBa_K561001</partinfo>), but we found no suitable lactate-induced promoter. Therefore, we decided to convert the promotor regulating the lldPRD operon in ''E.coli'' into a biobrick, and to use this biobrick in our project [[http://www.ncbi.nlm.nih.gov/pubmed/18263722 1]].<br />
<br />
The primers used to amplify the sequence are given below:<br />
<br />
{|border="1"<br />
!Primer<br />
!Sequence<br />
|-<br />
|Plld EcR fwd<br />
|GTTTCTTCGAATTCGCGGCCGCTTCTAGAGcacattcctataggccgagtaaggt<br />
|-<br />
|Plld EcR rev<br />
|GTTTCTTCCTGCAGCGGCCGCTACTAGTAtgcaggtctcctggagtccacgc<br />
|}<br />
<br />
The capitalized letters of the primer sequences corresponds to the biobrick prefix and suffix. As template, we used the ''E.coli K12'' genome sequence provided by the NCBI nucleotide database [[http://www.ncbi.nlm.nih.gov/nuccore/U00096.2 2]]. These primers in combination with the genome from ''E.coli'' K12 MG1655, yielded a biobrick consisting of the lld promoter including RBS (We called this brick Plld EcR, Ec because it is amplified from ''E.coli'', R because it contains RBS).<br />
<br />
We did not have sufficient time to test the Plld EcR biobrick, but it was sent to sequencing in the official shipping plasmid, pSB1C3, and the sequencing result had a 100 % match with the theoretical sequence of the amplified Plld + RBS sequence in pSB1C3.<br />
<br />
<br />
===ldhA promoter + RBS from ''C.glutamicum'' (<partinfo>BBa_K822001</partinfo>)===<br />
<br />
We also amplified the ldhA promoter from ''Corynebacterium glutamicum''. This has similar properties as the lld promoter from ''E.coli'', so this promoter was also a candidate to being used as the lactate inducable promoter in our project.<br />
The ldhA promoter was amplified using the genome of ''C.glutamicum'' ATC 13032 as template, and the primers below:<br />
<br />
{|border="1"<br />
!Primer<br />
!Sequence<br />
|-<br />
|Plld CgR fwd<br />
|GTTTCTTCGAATTCGCGGCCGCTTCTAGAGctctgttgcttaaat<br />
|-<br />
|Plld CgR rev<br />
|GTTTCTTCCTGCAGCGGCCGCTACTAGTAggtgacctcttctctgaaacgg<br />
|}<br />
<br />
The promoter has not been properly characterized, but sequencing indicated a 100 % match with the theoretical sequence.<br />
<br />
<br />
{{:Team:NTNU_Trondheim/Templates/Sponsors}}<br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/Experiments_and_ResultsTeam:NTNU Trondheim/Experiments and Results2012-09-26T20:43:51Z<p>Rahmilale: /* Experiments and results */</p>
<hr />
<div>{{:Team:NTNU_Trondheim/Templates/Header}}<br />
<html><br />
<div class="container"><br />
<div class="page-header-top"><br />
<h1>Experiments and results <small>How we tested our components and what we found out</small></h1><br />
</div><br />
</div><br />
<br />
<br />
<div class="container main-container"><br />
</html><br />
__TOC__<br />
<br />
==Experiments and results==<br />
<br />
To make a genetic circuit releasing colicin as a response to a low oxygen level and a high lactate level, we needed several biobricks. For a detailed list of all biobricks present in our construct, see the [https://2012.igem.org/Team:NTNU_Trondheim/Biobricks biobricks page]. A sketch showing our final construct built from all the necessary biobricks is also given below:<br />
<br />
* Bilde<br />
<br />
Most of the biobricks we decided to use were already present in the registry, but we also needed biobricks with certain properties that were not present in the registry. These we had to make ourselves. The new bricks we made, and which we also characterized, are the following; <br />
. a protein coding brick for colicin E1, <br />
. a YFP-generator, a regulative LacI-generator, which is also an improvement of an already existing biobrick, <br />
. the lld promotor + RBS from ''E.coli'', <br />
. and the lld promotor + RBS from ''C.glutamicum''.<br />
<br />
This page will focus on the biobricks we have made, how we made them, and how we have characterized them to show that they work.<br />
<br />
<br />
===Colicin (<partinfo>BBa_K822002</partinfo>)===<br />
<br />
Colicin is the protein we have chosen as toxin in our bacterial anti-cancer-kamikaze device. <br />
<br />
<br />
===Regulative LacI generator (<partinfo>BBa_K822004</partinfo>)===<br />
<br />
We made this brick in an effort to improve an already existing biobrick. The brick we wanted to improve was <partinfo>BBa_K292006</partinfo>. The NTNU iGEM team 2011 tried to use this brick in their stress sensor, but did not get it to work. They also tried to test-cut it and investigate the fragments using gel electrophoresis, but the fragments were either not as expected. This is why we thought this biobrick was a good candidate for an improvement. <br />
Since it is a composite part, we cloned it together again from scratch, using RBS (<partinfo>BBa_B0030</partinfo>), LacI (<partinfo>BBa_C0012</partinfo>) and a double terminator (<partinfo>BBa_B0014</partinfo>).<br />
<br />
When the cloning work was done, we sent both our new biobrick and the old one (<partinfo>BBa_K292006</partinfo>) to sequencing. The sequencing results can be found [https://2012.igem.org/Team:NTNU_Trondheim/Sequencing_Improved_Construct here]. The sequencing result shows that in the old biobrick, only the terminator is present, and no LacI or RBS. In our improved biobrick, both RBS, LacI and terminator are present.<br />
<br />
Both <partinfo>BBa_K822004</partinfo> and <partinfo>BBa_K292006</partinfo> was also investigated using gel electrophoresis. The gel pictures are given below:<br />
<br />
{|border="0"<br />
|[[File:Testkutt_BBa_K292006.png|x300px]]<br />
|[[File:RBS+LacI+term-gel.PNG|x300px]]<br />
|-<br />
|This is the test cut of BBa_K292006 that the NTNU iGEM team 2011 performed. The testcut was performed with EcoRI+PstI (expected fragments: 1303 bp + 2053 bp), BglI+BclI (expected fragments: 1324 bp + 2032 bp), BglI+EcoRV (expected fragments: 1596 bp + 1760 bp) and BglI+BanII (expected fragments: 1521 bp + 1835 bp). The test cut shows that none of the expected fragments are present.<br />
|Test cut of our improved part performed with NotI (first red box, expected fragments: 1276 bp + 2055 bp) and XbaI+PstI (second red box, expected fragments: 1278 bp + 2053 bp). The fragments cut with NotI makes sense on gel. In the case of cutting with XbaI+PstI, we did not expect three fragments, but the upper fragment could be uncut plasmid, since the lower fragments makes sense. <br />
|}<br />
<br />
<br />
===lld promoter + RBS from ''E.coli'' (<partinfo>BBa_K822000</partinfo>)===<br />
<br />
The two criteria we wanted fulfilled to initiate lysis and subsequent release of colicin were a low oxygen level and a high lactate level. A promoter activated by low oxygen level was already present in the registry (microaerobic Vgb promoter, <partinfo>BBa_K561001</partinfo>), but we found no suitable lactate-induced promoter. Therefore, we decided to convert the promotor regulating the lldPRD operon in ''E.coli'' into a biobrick, and to use this biobrick in our project [[http://www.ncbi.nlm.nih.gov/pubmed/18263722 1]].<br />
<br />
The primers used to amplify the sequence are given below:<br />
<br />
{|border="1"<br />
!Primer<br />
!Sequence<br />
|-<br />
|Plld EcR fwd<br />
|GTTTCTTCGAATTCGCGGCCGCTTCTAGAGcacattcctataggccgagtaaggt<br />
|-<br />
|Plld EcR rev<br />
|GTTTCTTCCTGCAGCGGCCGCTACTAGTAtgcaggtctcctggagtccacgc<br />
|}<br />
<br />
The capitalized letters of the primer sequences corresponds to the biobrick prefix and suffix. As template, we used the ''E.coli K12'' genome sequence provided by the NCBI nucleotide database [[http://www.ncbi.nlm.nih.gov/nuccore/U00096.2 2]]. These primers in combination with the genome from ''E.coli'' K12 MG1655, yielded a biobrick consisting of the lld promoter including RBS (We called this brick Plld EcR, Ec because it is amplified from ''E.coli'', R because it contains RBS).<br />
<br />
We did not have sufficient time to test the Plld EcR biobrick, but it was sent to sequencing in the official shipping plasmid, pSB1C3, and the sequencing result had a 100 % match with the theoretical sequence of the amplified Plld + RBS sequence in pSB1C3.<br />
<br />
<br />
===ldhA promoter + RBS from ''C.glutamicum'' (<partinfo>BBa_K822001</partinfo>)===<br />
<br />
We also amplified the ldhA promoter from ''Corynebacterium glutamicum''. This has similar properties as the lld promoter from ''E.coli'', so this promoter was also a candidate to being used as the lactate inducable promoter in our project.<br />
The ldhA promoter was amplified using the genome of ''C.glutamicum'' ATC 13032 as template, and the primers below:<br />
<br />
{|border="1"<br />
!Primer<br />
!Sequence<br />
|-<br />
|Plld CgR fwd<br />
|GTTTCTTCGAATTCGCGGCCGCTTCTAGAGctctgttgcttaaat<br />
|-<br />
|Plld CgR rev<br />
|GTTTCTTCCTGCAGCGGCCGCTACTAGTAggtgacctcttctctgaaacgg<br />
|}<br />
<br />
The promoter has not been properly characterized, but sequencing indicated a 100 % match with the theoretical sequence.<br />
<br />
<br />
{{:Team:NTNU_Trondheim/Templates/Sponsors}}<br />
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</div></div></html><br />
{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/ProjectTeam:NTNU Trondheim/Project2012-09-26T20:39:50Z<p>Rahmilale: /* Parts */</p>
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<h1>Project description <small>Bacterial Anti-Cancer Kamikaze explained</small></h1><br />
</div><br />
</div><br />
<br />
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<div class="container main-container"><br />
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__TOC__<br />
==Background==<br />
<br />
Cancer is the leading cause of death worldwide. In 2008 alone, 13% of all deaths (7,6 million people) were caused by cancer, and it is not likely that the number will decrease. Lifestyle diseases, for instance, are huge risk factors for developing cancer, and diseases like type 2 diabetes are increasing rapidly on a worldwide basis. [http://www.who.int/gho/publications/world_health_statistics/2012/en/index.html], [http://www.who.int/mediacentre/factsheets/fs312/en/].<br />
<br />
One of the most challenging aspects of cancer medicine is the difficulty of drug delivery directly at the tumor area. We therefore wanted to develop a system for specific drug delivery, to show that one of the most challenging medical problems can be solved by using synthetic biology. So we decided to make a system responding to factors specific for cancer cells, but without being too complicated [http://mct.aacrjournals.org/content/4/10/1636.full].<br />
In our system we want two different trigger factors, in order to lower the risk of releasing toxins in the healthy parts of the body. Our system is triggered by a low oxygen concentration and a high lactate concentration. When the ''E. coli'' detects these conditions, our system will activate the lysis genes, and the toxin will be released.<br />
<br />
Differentiated cells (“normal” cells) can produce high amount of lactate in an anaerobic environment, but this is not a normal environment for the cells in our body. Under normal circumstances, the differentiated cells will primarily metabolize glucose to carbon dioxide in the citric acid cycle (TCA), and have a very low production of lactate. Cancer cells behave differently. They produce large amounts of lactate regardless of the oxygen concentration in their surroundings [http://www.ncbi.nlm.nih.gov/pubmed/19460998], [http://cancerres.aacrjournals.org/content/58/7/1408.full.pdf+html]. The reason that we want to use oxygen as a trigger factor is that tumors exists in an environment deprived of oxygen [http://www.springerlink.com/content/a60537w7085574v4/].<br />
<br />
==Overview==<br />
<br />
Our goal for this years competition is to create a genetic circuit which enables ''E. coli'' cells to detect and attack cancer cells. To do this, the cells should produce a tumor inhibitor or toxin effective at killing cancer cells, and respond to environmental cues indicating the presence of cancer cells by undergoing [http://en.wikipedia.org/wiki/Lysis lysis], releasing the anti-cancer agent into the surrounding environment. In principle, bacteria could be used in "search and destroy" missions against cancer inside the human body. We wish to develop our genetic circuit as a proof-of-concept of one such strategy.<br />
<br />
A sketch of our current planned design for the circuit is shown below.<br />
<br />
[[File:Grønn_krets.png|thumb|center|600px|A sketch of our planned genetic circuit]]<br />
<br />
Ideally, the toxin should only be released if cancer cells are actually encountered, and never otherwise. To achieve this, the lysis-inducing part of the circuit should be regulated such that it is highly unlikely to be activated in other situations. One possible way is to use a signal molecule that is solely associated with cancer cells to activate the lysis device. Another possibility is to use a combination of environmental cues that together indicate a high likelihood of cancer presence. We have chosen the latter strategy, and the environmental cues we aim to use are low O<sub>2</sub> and high lactate concentrations. <br />
<br />
Each of the two cues activates a separate gene, which encode different proteins. Together, these two proteins should activate the unit responsible for lysis. Therefore, if only one of the cues is present, the cell does not lyse, and toxin is not released in high levels. (Some leakage of toxin must be expected even under normal conditions with no activation of the circuit). Selective activation in the presence of cancer cells would be crucial for the concept to be effective in a medical situation. <br />
<br />
As shown in the sketch, we plan to express the toxin-producing gene with a constitutive promoter. This means that the toxin production is always active. Ideally, the toxin should be maximally effective against cancer cells and minimally toxic to the toxin-producing bacterial cell. We have evaluated several candidate molecules and decided to use the protein [http://proteopedia.org/wiki/index.php/Colicin_E1 Colicin E1].<br />
<br />
==Details==<br />
<br />
Below is a more detailed sketch of the circuit design ([https://2012.igem.org/File:NTNU_sketchlegend.jpg legend]). The environmental cues oxygen and lactate regulate the production of two regulatory proteins, LuxR and LuxI. Oxygen inhibits the production of LuxR, while lactate activates the production of LuxI. LuxI in turn catalyzes the formation of a homo-serine lactone (HSL) compound from S-Adenosyl Methionine (SAM) and Hexanoyl-ACP (Hex). When both LuxR and HSL is produced, they combine irreversibly to form a complex which activates the promoter in front of the lysis device (BioBrick part <partinfo>BBa_K112808</partinfo>, designed by the [https://2008.igem.org/Team:UC_Berkeley University of California Berkeley iGEM 2008] team).<br />
<br />
[[File:NTNU_sketch1b.jpg|thumb|600px|center| Detailed overview of our genetic circuit.]] <br />
<br />
In order to have the presence of lactate activate the production of LuxI, we need a lactate-sensitive [http://en.wikipedia.org/wiki/Promoter_%28genetics%29 promoter]. We chose the lactate-sensitive promoter found in the [http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU164 lldPRD] operon of ''E. coli'' by PCR. However, the available literature indicates that this promoter [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC205257/ is repressed under low-oxygen conditions] due to the action of the ArcA regulatory protein. A possible solution is using site-directed mutagenesis to change the nucleotide sequence at the probable binding site of ArcA on the promoter to reduce its binding affinity and abolish its regulatory effect.<br />
<br />
==Challenges==<br />
The goal of making bacterial cells detect and attack cancer cells present several challenges.<br />
First, how can cancer cells be reliably and effectively detected? Early in the process after deciding on the goal, we considered using several human signalling molecules such as HGF and VEGF as cancer indicators, as these are known to be over-produced by tumors. However, we were unable to determine quickly if these would be able to enter and affect ''E. coli'' cells, due to their large size. In contrast, O<sub>2</sub> and lactate are small molecules which are easily taken up by the cells, and are known to directly regulate the expression of various genes.<br />
<br />
==Parts==<br />
===Promoters=== <br />
To allow our system to work correctly, several different promoters are needed. Of these, the most simple is a constitutive (always on) promoter in front of the toxin-producing gene. For this purpose, we have extracted the BioBrick part <partinfo>BBa_J23119</partinfo> from the iGEM DNA distribution kit. Second, a promoter having higher activity at low oxygen levels, similar to those found in tumors. As a candidate for this function, the vgb promoter BioBrick part <partinfo>BBa_K561001</partinfo> was tested. Thirdly, a promoter that is activated by lactate, a possible indicator of tumor cells in the vicinity. We cloned the lldPp promoter of the ''E. coli'' [http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU164 lldPRD] operon for this, as well as the corresponding promoter from ''Corynebacterium glutamicum''. Lastly, a promoter that is activated by a compound resulting from the activation of the previous two units. In our sketch, this compound is a LuxR-HSL complex, which can activate the promoters of several BioBrick parts, such as <partinfo>BBa_K145150</partinfo> or <partinfo>BBa_R0062</partinfo>.<br />
<br />
===Genes===<br />
LuxI is a acyl homoserine lactone syntase, an enzyme catalyzing the production of a homoserine lactone (HSL) from the precursors S-adenosyl methionine (Sam) and hexanoyl-ACP (Hex). The normal function of LuxI is as part of the bacterial lux system, a [http://en.wikipedia.org/wiki/Quorum_sensing quorom-sensing] system allowing cells in proximity to sense each others presence, estimate the local cell population and regulate [https://www.bio.cmu.edu/courses/03441/TermPapers/97TermPapers/lux/bioluminescence.html bioluminescence]. LuxI is available as the BioBrick part <partinfo>BBa_K092400</partinfo>.<br />
<br />
[[File:NTNU_3OHSL.gif|thumb|center|400px|[http://partsregistry.org/3OC6HSL 3-oxohexanoyl-homoserine lactone] is synthesized by LuxI]]<br />
<br />
LuxR is another protein in the lux system, and acts by binding to 3OC6HSL, the product formed by the catalytic activity of LuxI. LuxR-HSL then acts on gene promoters to regulate genetic expression. We will use the simultaneous expression of LuxR and LuxI leading to the the formation of LuxR-HSL to activate the lysis device which causes the cell to dissolve and release its produced toxin.<br />
<br />
The lysis device was made by the [https://2008.igem.org/Team:UC_Berkeley UC Berkeley iGEM 2008] team. The genes are from the [http://en.wikipedia.org/wiki/Enterobacteria_phage_T4 bacteriophage T4] (a virus that infects bacteria). We have placed the LuxR+HSL activated promoter in front of the part to control the initiation of cell lysis.<br />
<br />
[[File:S-Adenosyl methionine.png|thumb|center|300px|S-Adenoysyl-methionine (SAM)]]<br />
<br />
Colicin E1 is a type of Colicin, a bacteriocin made by ''E. coli'' which acts against other nearby ''E. coli'' to kill them by forming a pore in the membrane, leading to depolarisation of the membrane which kills the cell [http://www.proteopedia.org/wiki/index.php/Colicin_E1]. Previous iGEM results indicate that this colicin may be effective against mammalian cancer cells as well [https://2008.igem.org/Team:Heidelberg/Project/Killing_II#Colicin-Receiver].<br />
<br />
<br />
[[File:NTNU_ColicinE1_structure.png|thumb|300px|center|The structure of colicin E1.]]<br />
<br />
<br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}<br />
<!--The structure of Hexanoyl-ACP:<br />
[[file:HexanoylACP_structure.jpg|center|300px]] (from the RCSB Protein Databank, entry [http://www.rcsb.org/pdb/explore.do?structureId=2FAC 2FAC])--><br />
<br />
<!--==References==<br />
<br />
Lactate sensitive promoter:<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/18263722 Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli.]<br />
<br />
LuxI:<br />
<br />
[http://www.pnas.org/content/93/18/9505.full.pdf Generation of cell-to-cell signals in quorum sensing: Acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein]<br />
<br />
[http://www.genome.jp/dbget-bin/www_bget?ec:2.3.1.184 KEGG entry]<br />
<br />
LuxR:<br />
<br />
''Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators.''[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC205046/ J Bacteriol. 1994 January; 176(2): 269–275.]<br />
<br />
[http://www.uniprot.org/uniprot/P12746 Uniprot entry]<br />
<br />
[http://www.ncbi.nlm.nih.gov/protein/ADX97333.1 PubMed entry]<br />
<br />
Lysis device:<br />
<br />
[https://2008.igem.org/Team:UC_Berkeley/LysisDevice UC Berkeley iGEM 2008: Lysis Device]--></div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/ProjectTeam:NTNU Trondheim/Project2012-09-26T20:33:52Z<p>Rahmilale: /* Overview */</p>
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<h1>Project description <small>Bacterial Anti-Cancer Kamikaze explained</small></h1><br />
</div><br />
</div><br />
<br />
<br />
<div class="container main-container"><br />
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__TOC__<br />
==Background==<br />
<br />
Cancer is the leading cause of death worldwide. In 2008 alone, 13% of all deaths (7,6 million people) were caused by cancer, and it is not likely that the number will decrease. Lifestyle diseases, for instance, are huge risk factors for developing cancer, and diseases like type 2 diabetes are increasing rapidly on a worldwide basis. [http://www.who.int/gho/publications/world_health_statistics/2012/en/index.html], [http://www.who.int/mediacentre/factsheets/fs312/en/].<br />
<br />
One of the most challenging aspects of cancer medicine is the difficulty of drug delivery directly at the tumor area. We therefore wanted to develop a system for specific drug delivery, to show that one of the most challenging medical problems can be solved by using synthetic biology. So we decided to make a system responding to factors specific for cancer cells, but without being too complicated [http://mct.aacrjournals.org/content/4/10/1636.full].<br />
In our system we want two different trigger factors, in order to lower the risk of releasing toxins in the healthy parts of the body. Our system is triggered by a low oxygen concentration and a high lactate concentration. When the ''E. coli'' detects these conditions, our system will activate the lysis genes, and the toxin will be released.<br />
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Differentiated cells (“normal” cells) can produce high amount of lactate in an anaerobic environment, but this is not a normal environment for the cells in our body. Under normal circumstances, the differentiated cells will primarily metabolize glucose to carbon dioxide in the citric acid cycle (TCA), and have a very low production of lactate. Cancer cells behave differently. They produce large amounts of lactate regardless of the oxygen concentration in their surroundings [http://www.ncbi.nlm.nih.gov/pubmed/19460998], [http://cancerres.aacrjournals.org/content/58/7/1408.full.pdf+html]. The reason that we want to use oxygen as a trigger factor is that tumors exists in an environment deprived of oxygen [http://www.springerlink.com/content/a60537w7085574v4/].<br />
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==Overview==<br />
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Our goal for this years competition is to create a genetic circuit which enables ''E. coli'' cells to detect and attack cancer cells. To do this, the cells should produce a tumor inhibitor or toxin effective at killing cancer cells, and respond to environmental cues indicating the presence of cancer cells by undergoing [http://en.wikipedia.org/wiki/Lysis lysis], releasing the anti-cancer agent into the surrounding environment. In principle, bacteria could be used in "search and destroy" missions against cancer inside the human body. We wish to develop our genetic circuit as a proof-of-concept of one such strategy.<br />
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A sketch of our current planned design for the circuit is shown below.<br />
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[[File:Grønn_krets.png|thumb|center|600px|A sketch of our planned genetic circuit]]<br />
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Ideally, the toxin should only be released if cancer cells are actually encountered, and never otherwise. To achieve this, the lysis-inducing part of the circuit should be regulated such that it is highly unlikely to be activated in other situations. One possible way is to use a signal molecule that is solely associated with cancer cells to activate the lysis device. Another possibility is to use a combination of environmental cues that together indicate a high likelihood of cancer presence. We have chosen the latter strategy, and the environmental cues we aim to use are low O<sub>2</sub> and high lactate concentrations. <br />
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Each of the two cues activates a separate gene, which encode different proteins. Together, these two proteins should activate the unit responsible for lysis. Therefore, if only one of the cues is present, the cell does not lyse, and toxin is not released in high levels. (Some leakage of toxin must be expected even under normal conditions with no activation of the circuit). Selective activation in the presence of cancer cells would be crucial for the concept to be effective in a medical situation. <br />
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As shown in the sketch, we plan to express the toxin-producing gene with a constitutive promoter. This means that the toxin production is always active. Ideally, the toxin should be maximally effective against cancer cells and minimally toxic to the toxin-producing bacterial cell. We have evaluated several candidate molecules and decided to use the protein [http://proteopedia.org/wiki/index.php/Colicin_E1 Colicin E1].<br />
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==Details==<br />
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Below is a more detailed sketch of the circuit design ([https://2012.igem.org/File:NTNU_sketchlegend.jpg legend]). The environmental cues oxygen and lactate regulate the production of two regulatory proteins, LuxR and LuxI. Oxygen inhibits the production of LuxR, while lactate activates the production of LuxI. LuxI in turn catalyzes the formation of a homo-serine lactone (HSL) compound from S-Adenosyl Methionine (SAM) and Hexanoyl-ACP (Hex). When both LuxR and HSL is produced, they combine irreversibly to form a complex which activates the promoter in front of the lysis device (BioBrick part <partinfo>BBa_K112808</partinfo>, designed by the [https://2008.igem.org/Team:UC_Berkeley University of California Berkeley iGEM 2008] team).<br />
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[[File:NTNU_sketch1b.jpg|thumb|600px|center| Detailed overview of our genetic circuit.]] <br />
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In order to have the presence of lactate activate the production of LuxI, we need a lactate-sensitive [http://en.wikipedia.org/wiki/Promoter_%28genetics%29 promoter]. We will attempt to isolate the lactate-sensitive promoter found in the [http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU164 lldPRD] operon of ''E. coli'' by PCR. However, the available literature indicates that this promoter [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC205257/ is repressed under low-oxygen conditions] due to the action of the ArcA regulatory protein. A possible solution is using site-directed mutagenesis to change the nucleotide sequence at the probable binding site of ArcA on the promoter to reduce its binding affinity and abolish its regulatory effect.<br />
<br />
==Challenges==<br />
The goal of making bacterial cells detect and attack cancer cells present several challenges.<br />
First, how can cancer cells be reliably and effectively detected? Early in the process after deciding on the goal, we considered using several human signalling molecules such as HGF and VEGF as cancer indicators, as these are known to be over-produced by tumors. However, we were unable to determine quickly if these would be able to enter and affect ''E. coli'' cells, due to their large size. In contrast, O<sub>2</sub> and lactate are small molecules which are easily taken up by the cells, and are known to directly regulate the expression of various genes.<br />
<br />
==Parts==<br />
===Promoters=== <br />
To allow our system to work correctly, several different promoters are needed. Of these, the most simple is a constitutive (always on) promoter in front of the toxin-producing gene. For this purpose, we have extracted the BioBrick part <partinfo>BBa_J23119</partinfo> from the iGEM DNA distribution kit. Second, a promoter having higher activity at low oxygen levels, similar to those found in tumors. As a candidate for this function, the vgb promoter BioBrick part <partinfo>BBa_K561001</partinfo> was tested. Thirdly, a promoter that is activated by lactate, a possible indicator of tumor cells in the vicinity. We cloned the lldPp promoter of the ''E. coli'' [http://ecocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU164 lldPRD] operon for this, as well as the corresponding promoter from ''Corynebacterium glutamicum''. Lastly, a promoter that is activated by a compound resulting from the activation of the previous two units. In our sketch, this compound is a LuxR-HSL complex, which can activate the promoters of several BioBrick parts, such as <partinfo>BBa_K145150</partinfo> or <partinfo>BBa_R0062</partinfo>.<br />
<br />
===Genes===<br />
LuxI is a acyl homoserine lactone syntase, an enzyme catalyzing the production of a homoserine lactone (HSL) from the precursors S-adenosyl methionine (Sam) and hexanoyl-ACP (Hex). The normal function of LuxI is as part of the bacterial lux system, a [http://en.wikipedia.org/wiki/Quorum_sensing quorom-sensing] system allowing cells in proximity to sense each others presence, estimate the local cell population and regulate [https://www.bio.cmu.edu/courses/03441/TermPapers/97TermPapers/lux/bioluminescence.html bioluminescence]. LuxI is available as the BioBrick part <partinfo>BBa_K092400</partinfo>.<br />
<br />
[[File:NTNU_3OHSL.gif|thumb|center|400px|[http://partsregistry.org/3OC6HSL 3-oxohexanoyl-homoserine lactone] is synthesized by LuxI]]<br />
<br />
LuxR is another protein in the lux system, and acts by binding to 3OC6HSL, the product formed by the catalytic activity of LuxI. LuxR-HSL then acts on gene promoters to regulate genetic expression. We will use the simultaneous expression of LuxR and LuxI leading to the the formation of LuxR-HSL to activate the lysis device which causes the cell to dissolve and release its produced toxin.<br />
<br />
The lysis device was made by the [https://2008.igem.org/Team:UC_Berkeley UC Berkeley iGEM 2008] team. The genes are from the [http://en.wikipedia.org/wiki/Enterobacteria_phage_T4 bacteriophage T4] (a virus that infects bacteria). We have placed the LuxR+HSL activated promoter in front of the part to control the initiation of cell lysis.<br />
<br />
[[File:S-Adenosyl methionine.png|thumb|center|300px|S-Adenoysyl-methionine (SAM)]]<br />
<br />
Colicin E1 is a type of Colicin, a bacteriocin made by E. coli which acts against other nearby E. coli to kill them by forming a pore in the membrane, leading to depolarisation of the membrane which kills the cell [http://www.proteopedia.org/wiki/index.php/Colicin_E1]. Previous iGEM results indicate that this colicin may be effective against mammalian cancer cells as well [https://2008.igem.org/Team:Heidelberg/Project/Killing_II#Colicin-Receiver].<br />
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[[File:NTNU_ColicinE1_structure.png|thumb|300px|center|The structure of colicin E1.]]<br />
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<!--The structure of Hexanoyl-ACP:<br />
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<!--==References==<br />
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Lactate sensitive promoter:<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/18263722 Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli.]<br />
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LuxI:<br />
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[http://www.pnas.org/content/93/18/9505.full.pdf Generation of cell-to-cell signals in quorum sensing: Acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein]<br />
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[http://www.genome.jp/dbget-bin/www_bget?ec:2.3.1.184 KEGG entry]<br />
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LuxR:<br />
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''Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators.''[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC205046/ J Bacteriol. 1994 January; 176(2): 269–275.]<br />
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[http://www.uniprot.org/uniprot/P12746 Uniprot entry]<br />
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[http://www.ncbi.nlm.nih.gov/protein/ADX97333.1 PubMed entry]<br />
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Lysis device:<br />
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[https://2008.igem.org/Team:UC_Berkeley/LysisDevice UC Berkeley iGEM 2008: Lysis Device]--></div>Rahmilalehttp://2012.igem.org/Team:NTNU_Trondheim/TeamTeam:NTNU Trondheim/Team2012-09-26T20:28:36Z<p>Rahmilale: </p>
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<h1>Meet the team <small> Team NTNU Trondheim up close and personal</small></h1><br />
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<h1>The students</h1><br />
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<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>Graduated M.Sc. in Chemical engineering and biotechnology from NTNU, with specialization in biotechnology. <!--So now, I'm a graduate engineer (yay!). In my master thesis, I investigated the interaction between DNA and Uracil DNA Glycosylase, which is a repair enzyme removing uracil from DNA, using optical tweezers. I also just recieved a research stipend in medical imaging, meaning that for the next semester, I'll continue investigating single molecule interactions using optical tweezers.--></dd></div><br />
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<h2>Gunvor Røkke</h2><br />
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<dt>Interests outside academia:</dt><dd>Mainly playing the violin. I have been playing since I was five years old, and I am currently leading one of the three folk music orchestras in Trondheim. I also like to swim, or to gab with my friends.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>Team leader:</i> Teaching the other team members the basic cloning techniques used for biobrick assembly.</li><br />
<li><i>Team representative:</i> In case of interested journalists, I will talk to them. Rolf will be my manager and Nina my stylist! </li><br />
<li><i>Team dietitian:</i> One of my less serious responsibility areas is to make sure that all team members get their daily dose of carbohydrates (as we all agree that lowcarb is nonsense).</li></dd><br />
<dt>Fun fact:</dt><dd>I'm able to whistle and hum in two part harmony with myself. And no, I'm not mutated.</dd><br />
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<dt>Origin of replication:</dt><dd>Eidsvåg, Møre og Romsdal</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
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<h2>Nina Hole</h2><br />
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<dt>Interests outside academia:</dt><dd>Sports enthusiast, but especially interested in football. I also play football myself on NTNU's own football team. Other interests are reading, traveling and food.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul><li><i>Gunvor's stylist</i>:If Gunvor is representing the team, I have the main responsibility to do her make-up and so on.</li><li><i>Photo chief</i>: If something needs photographing, Nina is on the job!</li></ul><br />
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<dt>Fun fact:</dt><dd><br />
My favorite author/musician Jo Nesbø, has named his main character in his criminal novels Harry Hole. His inspiration for the last name comes from my family! </dd><br />
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<dt>Origin of replication:</dt><dd>Drammen</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
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<h2>Jarle Pahr</h2><br />
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<dt>Interests outside academia:</dt><dd>Aikido and psychology.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul><li><i>Master of the notebook:</i> Trying to get the other team members to update the notebook.</li><li><i>Cake chief: </i> Baking awesome cakes.</li></ul></dd><br />
<dt>Fun fact:</dt><dd>Is resistant to norovirus, thanks to a mutation in the FUT2 gene. Being a mutant is nice!</dd><br />
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<dt>Origin of replication:</dt><dd>Larvik</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
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<h2>Eirin Korvald</h2><br />
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<dt>Interests outside academia:</dt><dd>Music (both playing and listening), snowboarding, hiking, knitting, hanging with friends.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>iGEM hair dresser:</i> Making sure the entire team has fabulous hair at all times.</li></dd><br />
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<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in biotechnology.</dd></div><br />
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<h2>Ove Øyås</h2><br />
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<dt>Interests outside academia:</dt><dd>Nature, cycling, hiking, music, programming, being enthusiastic about stuff.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li><i>Internet chief:</i> Fixing the wiki and the Matchmaker. Making spaghetti code.</li></dd><br />
<dt>Fun fact:</dt><dd>Will easily eat raw ginger and garlic.</dd><br />
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<dt>Origin of replication:</dt><dd>Trondheim</dd><br />
<dt>Study program:</dt><dd>M.Sc. in Chemical engineering and biotechnology at NTNU, with specialization in applied theoretical chemistry.</dd></div><br />
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<h2>Rolf Heilemann Myhre</h2><br />
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<dt>Interests outside Academia:</dt><dd>In my spare time, I like exercising, hanging with friends, partying, movies etc. Also, I can't live without my computer.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul>Modelling the genetic circuit.</dd><br />
<dt>Fun fact:</dt><dd>I have not studied any biotechnology before joining the iGEM team.</dd><br />
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<h1>The advisors</h1><br />
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<dt>Origin of replication:</dt><dd>Stavanger, Norway</dd><br />
<dt>Position:</dt><dd>Professor</dd><br />
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<h2>Eivind Almaas</h2><br />
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<dt>Area of expertise:</dt><dd>Systems biology and network analysis</dd><br />
<dt>Interests outside academia:</dt><dd>Hiking, reading, living.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li>Team organization.</li><li>Computer modelling.</li></dd><br />
<dt>Fun fact:</dt><dd>Big fan of 50's Rock'n Roll and Rockabilly.</dd><br />
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<dt>Origin of replication:</dt><dd>Cologne, Germany</dd><br />
<dt>Position:</dt><dd>Postdoc.</dd><br />
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<h2>Rahmi Lale</h2><br />
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<dt>Area of expertise:</dt><dd>Transcriptional and translational regulation of bacterial gene<br />
expression, metabolic engineering. Metagenome/biodiscovery.</dd><br />
<dt>Interests outside academia:</dt><dd> Loves playing bass, likes biking/fishing/sailing, into web/graphic design.</dd><br />
<dt>Areas of responsibility:</dt><dd>Herding the nerds!</dd><br />
<dt>Fun fact:</dt><dd>He loves bugs so much that he makes his own kefir.</dd><br />
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<dt>Origin of replication:</dt><dd>Mannheim, Germany</dd><br />
<dt>Position:</dt><dd>Associate professor</dd></div><br />
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<h2>Martin Hohmann-Marriott</h2><br />
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<dt>Area of expertise:</dt><dd>Photosynthesis, bioenergetics, molecular biology.</dd><br />
<dt>Interests outside academia:</dt><dd>My family, history, all things computer and technology</dd><br />
<dt>Areas of responsibility:</dt><dd>Instructor, molecular biology and physiology<br />
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<dt>Fun fact:</dt><dd>Martin designed exercise equipment for ants as an undergraduate.</dd><br />
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<dt>Origin of replication:</dt><dd>Kristiansand, Norway</dd><br />
<dt>Position:</dt><dd>Doctoral student. Graduated M.Sc. in Physics and mathematics from NTNU.</dd><br />
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<h2>Marius Eidsaa</h2><br />
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<dt>Area of expertise:</dt><dd>Systems biology, mainly focusing on networks, both generally and in biology. I'm currently working on network methods and analysis of microarray data..</dd><br />
<dt>Interests outside academia:</dt><dd>I like to sing, and I'm currently singing tenor in two student-society based choirs. Other interests include music in general, food and drink and good company.</dd><br />
<dt>Areas of responsibility:</dt><dd><ul> <li>I'm a modelling instructor, so my main responsibility is to help set up and analyze our model.</li></dd><br />
<dt>Fun fact:</dt><dd>Has been swimming at a national level.</dd><br />
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{{:Team:NTNU_Trondheim/Templates/Footer}}</div>Rahmilalehttp://2012.igem.org/User:RahmilaleUser:Rahmilale2012-07-26T20:07:58Z<p>Rahmilale: Created page with "https://igem.org/User_Information.cgi?user_id=9324"</p>
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<div>https://igem.org/User_Information.cgi?user_id=9324</div>Rahmilale